Objectives The aim of the study was to analyse hair cortisol levels in cats whose owners had reported behavioural problems and undesirable behaviour. In addition, feline hair cortisol levels were compared between sexes, for indoor and outdoor cats and also for cats living in single or multi-cat households. Methods In total, 55 cats participated in the study, including 31 females and 24 males from various households. The cats belonged to 25 different owners who answered a questionnaire survey. The biological material used for the research were 2–3 cm fragments of hair removed at the level of the skin with scissors by the owners from the cats’ lumbosacral area. The cortisol concentration in the samples was determined with the DRG Salivary Cortisol HS ELISA. Statistical analysis of the results was performed with Statistica 13.3. Results A tendency toward lower cortisol levels was found in outdoor cats vs indoor cats (U = 251.5, P = 0.066). It was also found that the cats exhibiting behavioural problems (eg, house soiling [eliminating outside the litter box]) or aggressive behaviour towards household members had statistically significantly higher hair cortisol levels (U = 162.0 [P = 0.027] and U = 9.0 [P = 0.040], respectively). Conclusions and relevance High levels of stress in cats can affect their interactions with other cats and with humans. The incidence of undesirable behaviour was observed more frequently in indoor cats. Significantly higher cortisol levels were found in cats that eliminated outside the litter box or that showed aggression towards their owners.