The high protein content of formula offered to babies born with small weights is suspected to increase the risk of later obesity. This study examines the immediate and long term effects of neonatal diets differing in protein content on growth and adipose tissue features of pigs born with small birth weights. Piglets (10th percentile) were fed milk-replacers formulated to mimic sow milk (AP, 4.4 g of protein/100 kcal) or provide an excess of proteins (HP, 6.2 g of protein/100 kcal) from day 2 to weaning (day 28). Ten piglets were killed at day 28. Others piglets (n = 25) were then offered ad libitum a high fat diet (12% fat) up to day 160. From birth to weaning, HP piglets had a greater daily weight gain (P < 0.05). Relative weight of perirenal adipose tissue, mean adipocyte diameters and specific activities of lipogenic enzymes in perirenal and subcutaneous adipose tissues were lower (P < 0.05) in HP than in AP piglets at this age. Thereafter, growth performance did not differ between dietary groups. At day 160, percent body fat did not differ between HP and AP pigs. However, there was a trend towards greater proportion of enlarged adipocytes in perirenal and subcutaneous adipose tissues of HP pigs. Moreover, basal rates of glucose incorporation into adipocytes were lower in HP than in AP pigs. In summary, our data clearly show that a high protein formula induced a temporary reduction in adipose tissue development and altered adipose tissue physiology in the long-term.