Mindfulness meditation is an ancient and simple form of meditation that has been said to induce several important physical and psychological benefits. The present study was designed with the aim of investigating the psychobiological effects of mindfulness meditation practice in a clinical population. Sixteen patients with depression and anxiety symptoms were submitted to a mindfulness meditation programme for the period of 2 months. Psychological well‐being [5‐item Mental Health (MH‐5)] and several endocrine parameters [adrenocorticotropic hormone (ACTH), cortisol, dehydroepiandrosterone‐sulphate (DHEAS), thyroid‐stimulating hormone, triiodothyronine, thyroxine and parathyroid hormone (PTH)] were assessed before and after the meditation programme. At post‐test, the MH‐5 score improved, while the levels of DHEAS and ACTH were raised, and those of PTH decreased. Our results suggest that mindfulness meditation can exert a significant psychobiological modulation by enhancing psychological well‐being, as well as by regulating the levels of several hormonal parameters on different axes.