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The aim of this study was to evaluate the statistical process control (SPC) as an identification tool of non-natural effects on milk quality, which may be manipulated. Data of milk production, somatic cell count (SCC) and total bacterial count (TBC) from 384 farms were used. Natural effects (season and volume) on the variation of SCC and TBC were evaluated; furthermore, control charts of somatic cell score (SCS) and total bacterial count transformed (TBCt) were designed to find non-natural variation resources on four farms. It was observed that the season affected significantly the SCS and TBCt. Control charts, in each season, indicated the non-natural variation in SCS and TBCt on the four farms evaluated. Therefore, the application of SPC as a tool at farm level is an additional instrument for monitoring milk quality.