In the current study the microbiological, sensory and chemical properties of 24 kefirs (12 producers) from Estonian, Latvian and Lithuanian retail market were determined using gas chromatography (GC), high performance liquid chromatography (HPLC-MS/MS-Q-TOF and LC-ion trap MS/MS), spectrophotometry and other methods. Antihypertensive, angiotensin-converting enzyme (ACE) inhibiting, antioxidant and antibacterial peptides were found in the kefir samples. According to the results of principal component analysis of 200 most abundant compounds obtained with HPLC-MS/MS-Q-TOF analysis, Estonian kefirs differed from the rest. Kefirs of Latvian and Lithuanian origin showed similarities in several characteristics, probably related to the starter cultures and technological processes. The fatty acids composition of all Baltic kefirs was uniform. The antioxidant capacity of the kefirs varied slightly, whereas intermediate positive correlation (r = 0·32, P < 0·05) was found between antioxidativity and total bacterial count. The lipid oxidation level, estimated as the content of linoleic and oleic acid primary oxidation products, oxylipins, was very low in all studied kefirs. Only one third of analysed kefirs met the requirements of the minimum sum of viable microorganisms, indicated in the Codex Standard for Fermented Milks.