Fluctuating asymmetry (FA), an indicator of developmental instability, has been suggested to serve as a useful bioindicator of the fitness and condition of various groups of animals, including fish. The current study aimed to determine whether skeletal and body deformities of northern pike fry (3–12 cm standard length SL) reared under laboratory conditions imposed stress that was reflected in FA in otolith size (area). Although hatchery-reared fish were studied, FA also occurs in natural conditions and may indicate harmful effects of different environmental factors, including water pollution. Both the sagitta and lapillus were analyzed in fish with (n = 60) and without (n = 60) skeletal deformities. Despite the severity of deformity and extended duration of stress exposure (from hatching to ca. 2–3 months of life), there was no significant effect of the stressor on otolith FA, neither for sagittae nor lapilli. An overview of the literature indicated that links between stressors and fish otolith FA are not common (found in 9 out of 31 investigations). Thus, otolith FA is probably not an appropriate bioindicator for detecting the effects of different stressors, including pollution, despite previous suggestions.