Childhood malnutrition remains a public health issue in Indonesia with a national prevalence of wasting of 13% and stunting of 36%. In rural areas nutritional status depends on local agriculture and may fluctuate in relation to harvest time. The aim of this study was to characterise seasonal variations in nutritional status in two resettlement villages in the Oesao district, Nusa Tenggara Timur. A cross sectional study was conducted in a convenience sample of children after the wet season (March). Children aged 6 to 60 months were assessed for nutritional status using anthropometric and biochemical measures. A subset of these children was re-assessed for anthropometry after the dry season (November). Weight-for-height z scores improved significantly from mean±SD of -1.7± 0.9 in March to -1.3±0.9 in November (p<0.001). There was no significant change in height between seasons. Prevalence of wasting, (weight-for-height z score <-2), was 42% in March and 19% in November (p<0.001). However, stunting rates increased significantly from 42% in March to 45% in November (p<0.001). Thirty six per cent of children were anaemic (Hb level <11 mg/100 mL), 68% were vitamin A deficient (plasma vitamin A level <0.8 μmol/L) and 50% were zinc deficient (plasma zinc <9.94 μmol/L). All children except one were positive for intestinal parasites. These data indicate seasonal changes in anthropometry with inconsistent effects depending on the anthropometric index measured. Wasting and stunting were higher than the national average, alongside high rates of anaemia, zinc and vitamin A deficiencies.