The objective of this study was to investigate the effects of heating on the chemistry, physical properties and antifactor Xa activity of enoxaparin. Samples of enoxaparin heated at 70 degrees C lost 27% of their initial AFXa activity after 8 h, then activity increased to 94% of the initial activity over the next 4 h. Activity then decreased to 84% of control after 48 h and further to 80% of control over 22 days. The initial activity loss correlated with desulfation as demonstrated by sulfate and amine analysis. Fragmentation of oligosaccharides occurred, as demonstrated by reducing capacity and capillary electrophoresis analysis. Individual enoxaparin fractions obtained by high performance size exclusion chromatography were analysed. Early eluting fractions, containing aggregated oligosaccharides, increased in concentration following heating. Up to 65% of sulfate was lost from some fractions, containing hexa- and octa-saccharides, after 8 h, corresponding with decreased activity. Low mass oligosaccharide fractions increased in concentration and had increased activity between 8 and 12 h. Reversed-phase ion-interaction HPLC analysis supported these findings. Deca-, dodeca- and tetradeca-saccharides were resistant to thermal degradation. Desulfation, fragmentation and aggregation occur during the heating of enoxaparin and result in the initial rapid loss, recovery and subsequent gradual loss of activity.