The cytotoxic and antimicrobial activity of a series of six copper(II) complexes with phosphate and hydroxymethyl derivatives of pyridine and benzimidazole were investigated. The complexes and the corresponding free ligands were tested against Staphylococcus aureus ATCC 6538, Staphylococcus epidermidis ATCC 12228, Pseudomonas aeruginosa ATCC 15442, Escherichia coli ATCC 25922, Proteus hauseri ATCC 13315, and Candida albicans ATCC 10231. Among the tested copper(II) complexes, compounds 2 and 5 containing 1H‐benzimidazol‐2‐ylmethyl diethyl phosphate and 2‐(hydroxymethyl)benzimidazole as ligands, respectively, were most active and limited the growth of S. aureus, E. coli, and C. albicans by 30–60 % according to concentration and microorganism. The in vitro cytotoxic activity of the CuII complexes and free ligands towards cancerous B16 (murine melanoma) and non‐cancerous 10T1/2 (murine fibroblasts) cell lines was determined. The 10T1/2 cells were treated with the compounds at concentrations equal to IC50 values for B16 cells. In spite of the use of relatively high concentrations of the complexes, the viability of 10T1/2 cells was very high, ca. 80 % in some cases. Stability of the CuII complexes was evaluated in water solutions by UV/Vis spectroscopy. The copper(II) complex of 4‐(hydroxymethyl)pyridine was synthesized and identified.