The baseline selection is the first and important step to analyze magnetocardiography (MCG) parameters. There are no difficulties to select the baseline between P- and Q-wave peak (P-Q interval) of MCG wave recorded from healthy subjects because the P-Q intervals of the healthy subjects do not much vary. However, patients with ischemic heart disease often show an unstable P-Q interval which does not seem to be appropriate for the baseline. In this case, T-P interval is alternatively recommended for the baseline. However, there has been no study on the difference made by the baseline selection. In this study, we studied the effect of the different baseline selection. MCG data were analyzed from twenty healthy subjects and twenty one patients whose baselines were alternatively selected in the T-P interval for their inappropriate P-Q interval. Paired T-test was used to compare two set of data. Fifteen parameters derived from the R-wave peak, the T-wave peak, and the period, $T_{max/3}{sim}T_{max}$ were compared for the different baseline selection. As a result, most parameters did not show significant differences (p>0.05) except few parameters. Therefore, there will be no significant differences if anyone of two intervals were selected for the MCG baseline. However, for the consistent analysis, P-Q interval is strongly recommended for the baseline correction.