Milk quality criteria and limits for somatic cell count (SCC) established in many countries make it difficult to maintain SCC of bulk tank goat milk below the threshold, due to non-infection factors linked to goat physiology. The aim of this study was to objectively verify the effects of SCC on fresh caprine milk cheese. Somatic cells were recovered from pooled healthy goat milk, and added to low SCC raw or pasteurised goat milk. Miniature cheeses were made and evaluated after 1 and 7 d. Somatic cells had a major effect on lipolysis, increasing free fatty acids regardless of whether milk was raw or pasteurised. The effect of somatic cells on proteolysis was specific for caseins and the effects were different if cheeses are made from raw or pasteurised milk. It is concluded that somatic cells themselves in caprine milk can directly affect some cheese parameters.