Recent studies have implicated the habenula in modulating states of arousal and chronic responses to stress. We examined whether lesion of the habenula efferent pathway, the fasciculus retroflexus (FR), at either 3 (P3) or 70 (P70) days of age affects stress-related anxiety (elevated plus-maze test) and activity levels (open-field test) in rats tested as adults. Both P3- and P70-lesioned rats showed chronically elevated plasma levels of corticosterone. Rats receiving FR lesions as neonates (P3) exhibited greater open arm avoidance on the elevated plus-maze than controls 2 months postoperatively, suggesting a heightened state of anxiety. In contrast, P70-lesioned rats behaved similarly to controls on the plus-maze, but showed increased locomotion and increased grooming in the open field, effects not observed in P3-lesioned rats. When an additional stressful condition was imposed (5 days of social isolation plus 24 h food deprivation) before testing, both FR-lesion groups showed an attenuation of the normal behavioral responses (decreased open-arm entries/time in open arms, increased freezing). The effects of FR lesions on activity and behavioral indices of anxiety may be due to disruption of lateral habenular projections to dopaminergic neurons in the ventral tegmentum and/or projections to regions containing high concentrations of benzodiazepine receptors, the median and dorsal raphe and dorsal periaqueductal gray. Behavioral differences observed as a function of lesion age suggest differential capabilities of P3- and P70-lesioned rats to utilize compensatory mechanisms to correct FR lesion-induced deficits.