Background Undernutrition among under five children in India is a major public health problem.Despite India’s growth in the economy, the child mortality rate due to undernutrition is still high in both urban and rural areas.Studies that focus on urban slums are scarce. Hence the present study was carried out to assess the prevalence and determinants of undernutrition in children under five in Maharashtra, India.Methods A community-based cross-sectional study was conducted in 16 randomly selected clusters in two districts of Maharashtra state, India. Data were collected through house to house survey by interviewing mothers of under five children. Total 2929 mothers and their 3,671 under five children were covered. Multivariate logistic regression analysis was carried out to identify the determinants of child nutritional status seperately in urban and rural areas. Results The mean age of the children was 2.38years (±SD 1.365) and mean age of mothers was 24.25(± SD6.37) years.Overall prevalence of stunting among children under five was 45.9 %, wasting was 17.1% and 35.4% children were underweight.Prevalence of wasting, stunting and underweight were more seen in an urban slum than a rural area.In the rural areas exclusive breast feeding(p<0.001) and acute diarrhea (p=0.001)in children underfive were associated with wasting, children with birth order 2 or less than 2 were more affected by stunting and exclusive breast feeding (p<0.05) and low maternal education were associated with underweight.Whereas in the urban slums exclusive breast feeding(p<0.05) was associated with wasting, sex of the child (p<0.05) and type of family(p<0.05)were associated with stunting,and low income of the family(p<0.05) was associated with underweight.Conclusion Factors like sex of the child, birth order,exclusive breast feeding ,economic status of the family, type of family,acute diarrhea and maternal education have influence on nutritional status of the child. Improvement of maternal education will improve the nutritional status of the child. Strategies are needed to improve the economic status of the community.The trial registration-This article is part of baseline data of the project, hence not related to trial registration. After baseline data principal investigator had done trial registration retrospectively.