Systems and methods are described for on-line, real-time estimation of a residual mass in an engine cylinder during HCCI combustion. The residual mass is estimated based on an estimated residual mass for a previous combustion cycle. A value of a first performance variable for the first combustion cycle is determined based only on engine data measured by one or more sensors. A value of a second performance is estimated based at least in part on the estimated residual mass for the first combustion cycle. An adaptive scaling factor is determining for the first combustion cycle based on the determined value of the first performance variable and the estimated value of the second performance variable. An adjusted residual mass for the first combustion cycle is then determined based on the estimated residual mass for the first combustion cycle and the adaptive scaling factor for the first combustion cycle.