Background: Micronutrients are minerals and vitamins and they are essential for normal physiological activities. The objectives of the study were to describe the progress and determinants of micronutrient levels and to assess the effects of micronutrients in the treatment outcome of kalazar. Methods: A prospective cohort study design was used. The data were collected using patient interviews, measuring anthropometric indicators, and collecting laboratory samples. The blood samples were collected at five different periods during the leishmaniasis treatments: before starting anti-leishmaniasis treatments, in the first week, in the second week, in the third week, and in the 4th week of anti-leishmaniasis treatments. Descriptive statistics were used to describe the profile of patients and to compare the treatment success rate. The generalized estimating equation was used to identify the determinants of serum micronutrients.Results: The mean age of the patients were 32.88 years [SD (standard deviation) ±15.95]. Male constitute 62.3 % of the patients and problematic alcohol use was present in 11.5 % of the patients. The serum zinc level of visceral leishmaniasis patients was affected by alcohol (B -2.7 [95 % CI: -4.01 - -1.5]), DDS (B 9.75 [95 % CI: 7.71 – 11.79]), family size (B -1.63 [95 % CI: -2.68 - -0.58]), HIV (B -2.95 [95 % CI: -4.97 - -0.92]), and sex (B -1.28 [95 % CI: -2.5 - -0.07]). The serum iron level of visceral leishmaniasis patients was affected by alcohol (B 7.6 [95 % CI: 5.86 – 9.35]), family size (B -5.14 [95 % CI: -7.01 - -3.28]), malaria (B -12.69 [95 % CI: -14.53 - -10.87]), Hookworm (-4.48 [-6.82 - -2.14]), chronic diseases (B -7.44 [95 % CI: -9.75 - -5.13]), and HIV (B -5.51 [95% CI: -8.23 - -2.78]). The serum selenium level of visceral leishmaniasis patient was affected by HIV (B -18.1 [95 % CI: -20.63 - -15.58]) and family size (B -11.36 [95 % CI: -13.02 - -9.7]). The iodine level of visceral leishmaniasis patient was affected by HIV (B -38.02 [95 % CI: -41.98 - -34.06]), DDS (B 25 .84 [95 % CI: 22.57 – 29.1]), smoking (B -12.34 [95 % CI: -15.98 - -8.7]), chronic illness (B -5.14 [95 % CI: -7.82 - -2.46]), and regular physical exercise (B 5.82 [95 % CI: 0.39 - 11.26]). The serum vitamin D level of visceral leishmaniasis patient was affected by HIV (B -9.43 [95 % CI: -10.92 - -7.94]), DDS (B 16.24 [95% CI: 14.89 – 17.58]), malaria (B -0.61 [95 % CI: -3.37 - -3.37]), and family size (B -1.15 [95 % CI: -2.03 - -0.28]). The serum vitamin A level of visceral leishmaniasis patient was affected by residence (B 0.81 [95 % CI: 0.08 - 1.54]), BMI (B 1.52 [95 % CI: 0.42 – 2.6]), DDS (B 1.62 [95 % CI: 0.36 – 2.88]), family size (B -5.03 [95 % CI: -5.83 - -4.22]), HIV (B -2.89 [95% CI: -4.44 - -1.34]),MUAC (B 0.86 [95 % CI: 0.52 – 1.21]), and age (B 0.09 [95 % CI: 0.07 – 0.12]). Conclusion: The micronutrient levels of visceral leishmaniasis patients were significantly lower. The anti-leishmaniasis treatment did not increase the serum micronutrient level of the patients.