Utilizing randomly selected households of rural Honduran children ages 6 to 60 months, the objectives of this study were to determine 1) prevalence of stunting, wasting, and underweight, 2) factors associated with undernutrition, and 3) to geographically map prevalence’s of stunting and underweight by health center using latitude and longitude obtained via Global Positioning System (GPS). Randomized cross-sectional household surveys were conducted in 16 health centers in southwestern Honduras. Latitude, longitude and altitude were obtained at the household using a GPS. Geographic Information Systems—ArcGIS ® 9.2 software was used to create a series of maps of stunting and underweight by health center. 851 children participated and 56.8%, 20.8%, 1.6% of the children were stunted, underweight, and wasted, respectfully. Stunting and underweight were significantly associated with increasing age and altitude. Wasting decreased with increasing age. 57% of children were identified as having one, two, or all three of the growth deficiencies. Socioeconomic status indicators were significantly associated with stunting, underweight and wasting. Within the health centers of Hornitos, Cedritos, Mateo, and Arenalitos stunting was significantly more prevalent than that of the overall population and underweight was significantly higher in Hornitos, Cedritos, and Mateo. Wasting was significantly more prevalent in Santiago de Puringla and Hornitos. This is the first study reporting GPS mapping of the prevalence of stunting and underweight by health center in Honduras. Overall the prevalence of stunting is considered very high, underweight as high and wasting is low. Areas with the highest prevalence of undernutrition, mapped by health region, can be utilized by the Ministry of Healthy and other agencies to prioritize supplemental nutrition and education programs to areas at highest risk.