Protein malnutrition is particularly deleterious in young individuals. An immunodeficient state is a well‑known functional consequence but alterations in thymic morphology remain unknown. Our aim is to analyze morphological characteristics of the rat thymus in a perinatal undernutrition and renutrition model – we hypothesize these morphological alterations are reversible with early refeeding. Ninety-day-old Wistar rats were allowed to mate and divided into three groups: nourished (N – normal 20% protein diet), undernourished (UN – pre- and postnatal 5% protein diet until post-natal day 60 – PND 60) and renourished (RN – as UN but normal diet from PND 21 to 60). The thymi of 10 pups/group were submitted to macroscopic, histology, morphometry and scanning electron microscopy analyses. Body weight was highest in N and lowest in UN animals as expected but the thymic/body weight ratio remained similar in N and UN; this ratio was significantly higher in the RN group. UN thymi had a prevalence of type I collagen fibers, atrophic lobules and absence of a clear corticomedullary boundary. Thymic cortical component was decreased in UN. Apoptotic thymocytes were more frequently visualized in the UN thymi. N and RN thymi exhibited very similar morphology. Perinatal protein malnutrition induces drastic morphological alterations in rat thymi but these could be largely reversed with early renutrition. Functional studies are needed to assess if organ function mimics morphology in its recovery.