Synovial sepsis in horses is life threatening and accurate diagnosis allowing prompt treatment is warranted. This study assessed the diagnostic value of serum amyloid A (SAA) and D-lactate in blood and synovial fluid (SF) as diagnostic markers of synovial sepsis in horses and correlated them with total nucleated cell count (TNCC), percentage of neutrophils (%N) and total protein (TP) in SF. Blood and SF SAA and D-lactate concentrations were determined in a case–control observational study including 112 horses (38 with synovial contamination or sepsis (SCS), 66 with non-septic intra-synovial pathology (NSISP) and 8 controls). Blood and SF SAA were significantly higher in SCS than in NSISP and control horses. SAA values were similar in NSISP and control horses. SF SAA was moderately correlated with synovial TNCC, TP and blood SAA. Blood and SF SAA were 82.4 per cent and 80 per cent sensitive and 88.9 per cent and 73 per cent specific for diagnosis of SCS, with cut-off values of 60.7 and 1.14 µg/ml, respectively. Blood and SF D-lactate concentrations were not significantly different between groups. This study shows that blood and SF SAA concentrations can aid to distinguish SCS from non-septic synovial pathology; however, D-lactate was not useful.