A cross-sectional study was conducted to investigate the problem of nutritional status and intestinal helminthiasis among underfive children in three selected refugee centers in Kupang District, East Nusa Tenggara and to identify possible relationship between intestinal helminthiasis and nutritional status. A number of 188 children 12-59 months of age were involved in this study. All three refugee centers showed that Ascaris lumbricoides was most common (29.0% in Naibonat, 28.8% in Noelbaki and 23.4% in Tuapukan), followed by hookworm (25.8% in Naibonat, 10.0% in Noelbaki and 3.9% in Tuapukan) and the least common was Trichuris trichiura (6.3% in Noelbaki, 3.2% in Noelbaki and 0% in Tuapukan). Based on the WHO?s criteria the intensity of intestinalhelminthiasis in all three refugee centers were low. Nutritional status was characterized by high of prevalence of underweight, stunting and wasting in all three refugee centers. The prevalence of underweight was 28.6% in Tuapukan, 25.8% in Naibonat, and 18.8% in Noelbaki. The prevalence of stunting was 29.0% in Naibonat, 20% in Noelbaki and23.4% in Tuapukan. While the prevalence of wasting was 8.8% in Noelbaki, 6.5% in Naibonat and 3.9% in Tuapukan. For anemia, 75% of children in Noelbaki, 71.4% in Tuapukan and 45.2% in Naibonat had haemoglobin level less than 11 g/dl. There was no significant association between the prevalence of Ascaris lumbricoides and nutritional status of children also between the intensity of Ascaris Iumbricoides and nutritional status.