Male wild house mice selected for Short Attack Latency (SAL) show an active coping style to environmental challenges, whereas males selected for Long Attack Latency (LAL) generally exhibit a passive coping style. Previous studies showed that the aggressive SAL males develop routines more quickly and show more resistance to environmental changes than the less aggressive LAL ones; the latter behave more flexibly in non-social situations. Furthermore, using reciprocal F1s and backcross lines for SAL and LAL males, a Y chromosomal effect on aggression has been demonstrated. The aim of this study was to examine possible effects of the Y chromosome on behavioural flexibility. For this purpose six genotypes (SAL, LAL, their reciprocal F1s and their congenics for the non-pseudoautosomal part of the Y chromosome) were tested for their behavioural flexibility in a Y-maze. Differences between SAL and LAL were reproduced. Congenic lines showed identical scores to their parental ones. Regarding the reciprocal F1s, differences in aggression were not associated with behavioural flexibility. Therefore, it may be concluded that the Y chromosome does not influence aggression-related behavioural flexibility.