This paper develops a new approach to estimation of in-cylinder pressure and combustion variables for cycle-to-cycle combustion control in diesel engines. Such combustion control can lead to enhancement of engine performance and efficiency as well as prevention of combustion failures in UAV diesel engines. In-cylinder pressure and combustion variables are estimated using measurements from a non-intrusive accelerometer located on the engine block. The new estimation approach is based on separating the combustion component of the acceleration signal from the non-combustion component. A time-varying first order differential equation model relating the combustion components of acceleration and pressure is then utilized. The proposed method is evaluated using experimental data from a turbocharged high speed diesel engine. The robustness of the proposed estimation algorithm is demonstrated by evaluating it with 85 experimental data sets of many different operating conditions involving both single and double (pilot and main) injections. In-cylinder pressure and combustion variables such as cumulative heat release and crank angle of 50 percent cumulative heat release (CA50) are estimated, with CA50 being a key variable needed for closed-loop cycle-to-cycle combustion control. Experimental results show that the CA50 value is estimated accurately with an RMS error of 1.45 degrees in single injection data sets involving 40 different operating conditions and an RMS error of 3.96 degrees in double injection data sets involving 45 different operating conditions.