Nutritional problems represent one of the sequelae of the congenital abnormality of cleft lip± palate or cleft palate only and this may be aggravated by the high prevalence of protein energy malnutrition in our environment. A cross sectional study of the nutritional status of children with cleft lip± palate or cleft palate only aged three month to five years and those of non-cleft healthy children within the same age group and in the same environment was conducted in order to determine the effect of cleft on the nutritional status of children with non-sydromic cleft lip± palate or cleft palate only in Ile-Ife. The study was carried out at the Obafemi Awolowo University Teaching Hospitals Complex, Ile- Ife, Osun State, about 200 kilometres from Lagos, Nigeria from July 1, 2007 to June 30, 2008. A total of one hundred children was recruited into the study. Fifty children with the cleft deformities were recruited from the cleft clinic consecutively while the control group was made up of fifty non- cleft healthy normal children visiting the infant and under-5 welfare clinic for immunization and regular check-ups and selected using the simple random sampling technique. Clinical examination was performed on all the children to ascertain their suitability for inclusion into the study and their anthropometric measurements were taken thereafter. A researcher facilitated structured questionnaire was then used to obtain data on demography, socioeconomic status and feeding practices during infancy. The data was analysed using Epi-info programme and Statistical Package for Social Sciences. The prevalences of underweight, wasting and stunting for the cleft group were 26%, 18%, 14% respectively while that of the control group were 18%, 14%, 10% respectively using the World Health Organisation/ National Centre for Health Statistics (WHO/NCHS) cut off points. The difference in the prevalences of underweight, wasting and stunting between the two groups did not reach statistical significance as p= 0.334, 0.585 and 0.538 for underweight, wasting and stunting respectively with p value set as < 0.05. Using the mid upper arm circumference for age WHO cut off points, the prevalence of malnutrition was lower than for underweight for both the cleft group: 16%, and the control group: 4%. With the use of triceps skinfold thickness WHO cut off points however, the prevalence of malnutrition (cleft= 32%, control= 16%) is comparable to that obtained using underweight (cleft= 26%, control= 18%) as nutritional indicator. The observed difference in the prevalence of malnutrition between the two groups using TSFT for age and MUAC for age failed to reach statistical significance as p= 0.061 and 0.122 respectively. The cleft group was however found to have statistically significant lower prevalence of breastfeeding, p=0.000 and statistically significant higher prevalence of bottlefeeding with infant formula, p=0.000. From this study it can be concluded that although the prevalence of malnutrition in children with cleft lip ± palate or cleft palate only was clinically higher than the prevalence of malnutrition in a suitably matched control, the difference was not statistically significant. The preferential adoption of bottlefeeding with infant formula by the majority in the cleft population may however be responsible for the comparable prevalence of malnutrition in the cleft group. To this end, the use of bottle feeding with infant formula where satisfactory feeding with breastmilk cannot be achieved, regular monitoring of growth and nutritional parameters, and a large sample size prospective study to further evaluate the impact of the different types of cleft on the nutritional status of the children with cleft deformities are recommended.