Handling systems can influence the production of biogas and methane from dairy farm manures. A comparative work performed in three different Italian dairy farms showed how the most common techniques (scraper, slatted floor, flushing) can change the characteristics of collected manure. Scraper appears to be the most neutral choice, as it does not significantly affect the original characteristics of manure. Slatted floor produces a manure that has a lower methane potential in comparison with scraper, due to: a lower content of volatile solids caused by the biodegradation occurring in the deep pit, and a lower specific biogas production caused by the change in the characteristics of organic matter. Flushing can produce three different fluxes: diluted flushed manure, solid separated manure and liquid separated manure. The diluted fraction appears to be unsuitable for conventional anaero-bic digestion in completely stirred reactors (CSTR), since its content of organic matter is too low to be worthwhile. The liquid separated fraction could represent an interesting material, as it appears to accumulate the most biodegradable organic fraction, but not as primary substrate in CSTR as the organic matter concentration is too low. Finally, the solid-liquid separation process tends to accumulate inert matter in the solid separated fraction and, therefore, its specific methane production is low.