This study investigated whether compensatory growth causes long-term effects in relative brain- or intestine size in a wild, predominantly anadromous, population of brown trout (Salmo trutta). The subject fish belonged to two treatment groups; one group had undergone starvation and subsequent growth compensation, while the other were unrestricted controls. The main hypothesis that compensatory growth would negatively affect brain and intestinal size, as a consequence of growth trade-offs during the compensatory phase, could not be supported as no significant differences were detected between the treatment groups. Further exploratory analyses suggested that males and females started to diverge in both brain and intestine size at around 130 mm fork length, with females developing relatively smaller brains and larger intestines. The size at which the differences appear is a typical size for smoltification (saltwater preadaptation), and females tend to smoltify to a higher proportion than males. Smoltification is known to cause a more elongated morphology and relatively smaller heads in salmonids, and the marine lifestyle is associated with rapid growth, which could require relatively larger intestines. Hence, these emerging sex differences could be a consequence of sex-biased smoltification rates. An investigation of wild smolts of both sexes indicated no differences in brain or intestine mass between male and female smolts.