Major Diseases of Nepal: Burden, Elimination Targets and Prevention

Nepal's infectious-disease landscape is shaped by its geography: a hot, humid, mosquito-friendly Tarai plain along the open Indian border, temperate mid-hills, and cold high mountains. Vector-borne and neglected tropical diseases concentrate in the Tarai, while waterborne infections such as typhoid and cholera cluster in dense, poorly sewered cities like the Kathmandu Valley. Climate change, urbanisation and cross-border movement are steadily redrawing where these diseases occur, pushing some, such as dengue, kala-azar and Japanese encephalitis, into the hills and cities where they were once rare.

The lead agency for disease control is the Epidemiology and Disease Control Division (EDCD) under the Department of Health Services, Ministry of Health and Population. EDCD runs national programmes for malaria, kala-azar, lymphatic filariasis, leprosy and other conditions, while the National Tuberculosis Control Centre handles TB. Nepal has committed, alongside the World Health Organization (WHO) South-East Asia Region, to eliminate several of these diseases as public-health problems within this decade.

This directory profiles twelve diseases of national significance: malaria, kala-azar (visceral leishmaniasis), lymphatic filariasis, leprosy, tuberculosis, typhoid, cholera and acute gastroenteritis, scrub typhus, Japanese encephalitis, chikungunya, rabies and COVID-19. Dengue and tuberculosis have their own detailed pages on this site and are summarised only briefly here.

Malaria is a parasitic disease caused by Plasmodium species and transmitted by the bite of infected female Anopheles mosquitoes. Symptoms include recurring fever with chills, headache, body ache, sweating and, in severe cases, anaemia and organ failure. In Nepal, transmission is concentrated in forested foothill and inner-Tarai districts, and the country distinguishes between indigenous (locally acquired) cases and imported cases, most of which arrive with migrant workers returning from India and beyond.

Nepal committed to eliminating malaria by 2026, which required driving indigenous transmission to zero and sustaining that for three consecutive years. That goal has proved unattainable: the EDCD reported 528 cases in 2023 (23 indigenous) and 1,043 cases in 2024 (37 indigenous and 1,006 imported). With cases rising rather than falling, authorities have signalled the target will be pushed to 2030, aligning with the WHO deadline. Officials blame imported cases across the open southern border, budget constraints and climate-driven changes in mosquito range, making cross-border screening of returning migrants central to keeping elimination on track.

Kala-azar, or visceral leishmaniasis (locally kalajwar), is caused by the Leishmania donovani parasite and spread by the bite of tiny sandflies (Phlebotomus argentipes). It attacks the internal organs, causing prolonged fever, weight loss, an enlarged spleen and liver, and anaemia, and is usually fatal if untreated. Nepal launched a national elimination plan in 2005 targeting fewer than one case per 10,000 people at district level, and in 2013 became the first country in the region to reach that threshold across its officially endemic Tarai districts.

Elimination has since faced last-mile challenges. Since 2017 several previously non-endemic hill districts have breached the threshold, and cases have appeared in the mid-hills and even the Kathmandu Valley, a sign the sandfly's range is shifting. Reported cases were 216 in 2019, 186 in 2020 and 212 in 2021, and a few implementation units remained above target as of 2023. Nepal, with India and Bangladesh, is working toward regional elimination of kala-azar, with the current WHO South-East Asia deadline set for 2026.

Lymphatic filariasis (hattipaile or elephantiasis) is caused by the thread-like worm Wuchereria bancrofti, transmitted by Culex mosquitoes. The worms damage the lymphatic system and years later can cause gross swelling of the legs and genitals (lymphoedema and hydrocele) and lasting disability. Sixty-one districts of Nepal were mapped as endemic, and EDCD began mass drug administration (MDA) of diethylcarbamazine plus albendazole in Parsa district in 2003, scaling up nationwide by 2013.

The programme has been one of Nepal's biggest public-health successes: MDA has now been stopped in 57 endemic districts after they fell below the 1% microfilaria threshold, and recent assessments found antigen positivity of about 0.45% and microfilaria prevalence of just 0.05% in surveyed areas. A few high-risk municipalities still show transmission, prompting fresh MDA rounds in early 2026. Nepal aims to eliminate lymphatic filariasis as a public-health problem by 2030.

Leprosy (kustharog), caused by the slow-growing bacterium Mycobacterium leprae, mainly affects the skin, peripheral nerves and eyes, producing pale or reddish patches with loss of sensation and, if untreated, permanent nerve damage and deformity. It is curable with free multidrug therapy (MDT). Nepal eliminated leprosy as a public-health problem at the national level in 2009, formally declared on 19 January 2010, when registered prevalence fell to 0.77 cases per 10,000 people. New cases have kept falling, with a roughly 25% decline in annual new cases between 2019 and 2023/24.

National elimination, however, masks stubborn pockets. Around 17 districts and three provinces, home to roughly 41% of Nepal's population, have yet to reach the threshold, with Madhesh Province accounting for about 40% of cases and Lumbini around 18%. Continued transmission and late diagnosis, especially in children, show leprosy is not yet a disease of the past in the Tarai, even as the number of municipalities reporting zero cases rose from 65 in 2019 to 353 in 2023/24.

Tuberculosis (TB, kshaya rog) remains one of Nepal's heaviest infectious burdens. Caused by Mycobacterium tuberculosis and spread through the air when infected people cough, it typically causes a persistent cough, fever, night sweats and weight loss. WHO estimates on the order of 70,000 new cases each year, yet the National Tuberculosis Programme notified only about 40,000 patients in 2023, leaving a large 'missing' case gap that fuels ongoing transmission. TB has a dedicated page on this site with fuller detail.

Typhoid fever (typhoid, motijara) is a systemic infection caused by Salmonella enterica serovar Typhi, spread through food and water contaminated with faeces. It causes sustained high fever, headache, abdominal pain, weakness and, without treatment, dangerous intestinal complications. Nepal is a high-burden country, with estimated incidence well above the WHO threshold of 100 cases per 100,000 people per year. In 2022 Nepal introduced the typhoid conjugate vaccine (TCV) into its national immunisation schedule, which has sharply cut disease in vaccinated children.

Cholera is an acute diarrhoeal infection caused by the bacterium Vibrio cholerae, which can kill within hours through severe dehydration if untreated. It is one severe form of acute gastroenteritis (AGE), the seasonal diarrhoeal illness that surges every monsoon. Nepal records recurring cholera outbreaks, including large clusters in Kapilvastu and, more recently, Birgunj, and authorities have flagged at least 30 districts, including all three Kathmandu Valley districts, as highly vulnerable.

The root cause is water quality: studies after outbreaks found that a large majority of drinking-water samples in the Kathmandu Valley were contaminated with E. coli and faecal coliforms. Prevention centres on safe drinking water, hand hygiene, food safety, oral rehydration therapy for diarrhoea, oral cholera vaccine in high-risk settings, and improved sewerage.

Japanese encephalitis (JE) is a mosquito-borne viral brain infection spread by Culex mosquitoes in a cycle involving pigs and water birds. Most infections are mild, but a small share progress to encephalitis with high fever, seizures, coma and lasting neurological damage. Nepal introduced the SA 14-14-2 JE vaccine through mass campaigns from 2006 and later added it to routine childhood immunisation, dramatically reducing cases. Outbreaks continue, and an unusual 2024 outbreak recorded dozens of confirmed cases and around 17 deaths, spreading into the Kathmandu Valley, with under half of patients found to have been vaccinated.

Scrub typhus, caused by the bacterium Orientia tsutsugamushi and transmitted by the bite of larval mites (chiggers), has emerged as a notable cause of fever and encephalitis in Nepal, with more than 2,200 cases reported in 2023; it responds well to antibiotics such as doxycycline if caught early. Chikungunya, a viral illness spread by Aedes mosquitoes and causing fever with severe, sometimes prolonged joint pain, has also risen; between January and August 2025 Nepal reported 732 suspected and 400 laboratory-confirmed cases, mostly in urban areas.

Rabies is a nearly always fatal viral disease transmitted mainly through the bite or scratch of infected dogs. Nepal has pledged to eliminate dog-mediated human rabies deaths by 2030 under a One Health strategy, but dog-bite cases have surged from roughly 42,000 in 2014 to more than 81,000 a year by 2024. Official records list only around 10 to 32 human deaths annually, while experts believe the true toll is 100 to 200 because many rural victims die at home. Rabies is entirely preventable: wash bite wounds thoroughly, seek post-exposure vaccination immediately, and vaccinate dogs.

COVID-19, caused by the SARS-CoV-2 coronavirus, arrived early in Nepal: the country confirmed its first case on 23 January 2020 in a student returning from Wuhan, the first recorded case in South Asia, and its first death on 14 May 2020. The virus spreads mainly through respiratory droplets and aerosols, causing fever, cough, fatigue and loss of smell, with severe pneumonia and death most likely in older people and those with chronic illness.

Nepal endured severe waves, most devastatingly the Delta-driven surge of 2021 that overwhelmed hospitals and oxygen supplies. Vaccination began on 27 January 2021 and eventually reached most of the adult population. By the time routine global tracking wound down in April 2024, Nepal had reported over one million cumulative cases and around 12,000 deaths, figures widely regarded as undercounts given limited testing. COVID-19 is now managed as an endemic respiratory infection, leaving a legacy of stronger laboratory and surveillance capacity.

Across this whole list, a handful of measures prevent most infections: vaccination where available, clean water and sanitation, vector control, personal protection against bites, and prompt diagnosis and treatment. Diseases that are vaccine-preventable in Nepal today include Japanese encephalitis, typhoid (TCV), cholera (oral vaccine in outbreaks), COVID-19 and rabies (as post-exposure treatment). Nepal's formal elimination goals, summarised in the facts table, all depend on closing surveillance gaps, sustaining funding and improving basic water and sanitation.

Anyone with a high fever lasting more than a couple of days, an animal bite, severe or bloody diarrhoea, or a stiff neck with confusion should seek medical care promptly rather than self-treating, as early treatment saves lives across nearly all of these conditions. Free or subsidised diagnosis and medicines are available through government facilities for TB, leprosy, kala-azar, malaria and rabies post-exposure care, so cost should not be a barrier to timely care.