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Background Papua New Guinea (PNG) is one of the nutritionally vulnerable countries with a high rate of children death without showing a sign of improvement in last two decades. Current study investigated the prevalences of stunting and wasting among a cohort of children in PNG and described the spatial features of these outcomes at the province and district-levels. Objective To determine the prevalences of stunting and wasting among a cohort of children in PNG and to describe the spatial features of these outcomes at the province and district-levels. We also described the spatial features of these outcomes at province and district-levels. Methods The health and nutritional status of 683 children aged less than five years was assessed using a cross-sectional multi-stage household survey conducted in the Eastern Highlands and Madang Provinces of PNG during the period of 2003–2004. Growth z-scores such as height-for-age and weight-for-age were generated using World Health Organization classifications. Results The prevalences of stunting (height-for-age z-score less than −2.0) were 59% and 49% in the Eastern Highlands and Madang respectively (P = 0.019). The prevalences of wasting (weight-for-height z-score less than −2.0) were 14% and 22% in Eastern Highlands and Madang respectively, (P = 0.039); overall, only 21% of the children had completed all their scheduled vaccines and 95% of the caregivers had less than primary school education. Our statistical maps showed considerable spatial variations (province- and district-levels) with regard to the stunting, wasting and other key factors within a relatively small geographical region. Conclusions Current study determined one of the highest prevalence of stunting among children in PNG. The impact of geographical locations on the risk factors must be recognized as it affects epidemiology and intervention coverage.