Cylinder pressure measurements are common practice for internal combustion reciprocating engines during field or lab applications for the purpose of combustion analysis, condition monitoring etc. The most accurate method is to measure cylinder pressure using a crank angle encoder as a trigger source to guarantee cylinder pressure measurement at predefined crank angle events. This solution, even though favorable, presents a number of practical difficulties for field applications and increased cost, for this reason its use is practically restricted to lab applications. Therefore a commonly used approach for ad hoc measurements is to digitize samples at fixed time intervals and then convert time into crank angle assuming a constant rotational speed. But if engine rotational speed is not constant within the engine cycle this may result to incorrect cylinder pressure CA referencing. To identify the error introduced from improper cylinder pressure CA phasing, and to propose methods to minimize the negative impact on the measured cylinder pressure traces, an experimental setup has been developed based on a single cylinder prototype DI diesel engine. Measurements were performed using the two aforementioned technical solutions with simultaneous measurement of the engine instantaneous rotational speed. The direct comparison of the two sets of measured cylinder pressure traces reveals the introduced indexing error. Following this, an attempt is made to propose a correction methodology based on the estimation of the engine instantaneous rotational speed. For its estimation three different methods are proposed and evaluated. The first method makes use of a low resolution instantaneous speed signal, provided by a sensor reading marks on the engine flywheel, the second makes use of the BDC and TDC events and the third is based on the comparison of the duration of the compression and expansion phases. As revealed from the analysis all three methods results to a reduction of the error induced in the estimation of Indicated Work by a magnitude of 10 times i.e. from up to 7% to less than 1%.