Hypothermic machine perfusion (HMP) is increasingly used in deceased-donor kidney transplantation, but controversy exists regarding the value of perfusion biomarkers and pump parameters for assessing organ quality. We prospectively determined associations between perfusate biomarkers [neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), interleukin-18 (IL-18) and liver-type fatty acid-binding protein (L-FABP)] and pump parameters (resistance and flow) with outcomes of delayed graft function (DGF) and 6-month estimated glomerular filtration rate (eGFR). DGF occurred in 230/671 (34%) recipients. Only 1-hour flow was inversely associated with DGF. Higher NGAL or L-FABP concentrations and increased resistance were inversely associated with 6-month eGFR, while higher flow was associated with higher adjusted 6-month eGFR. Discarded kidneys had consistently higher median resistance and lower median flow than transplanted kidneys, but median perfusate biomarker concentrations were either lower or not significantly different in discarded compared with transplanted kidneys. Notably, most recipients of transplanted kidneys with isolated “undesirable” biomarker levels or HMP parameters experienced acceptable 6-month allograft function, suggesting these characteristics should not be used in isolation for discard decisions. Additional studies must confirm the utility of combining HMP measurements with other characteristics to assess kidney quality.