Current multi-detector CT and electron beam tomography (EBT) technology enables the evaluation of coronary calcification. Multiple software packages are available to quantify calcification using several scoring algorithms implementing user-definable scoring parameters. We investigated the effect of scoring parameters on the calcium score outcome. Three parameters (four-connected or eight-connected, lesion size threshold and interpolation) are evaluated. Their theoretical influence on the scoring outcome is shown using simplified examples. To evaluate the effect in real data, we performed calcium scoring on randomly chosen EBT scans from 50 participants in an epidemiological study. Both the Agatston and volume scores were calculated. Changing from eight-connected to four-connected connectivity decreased both Agatston and volume scores (mean variability Agatston 3.15% and volume score -3.52%). Decreasing the threshold from 4 to 2 pixels increased the calcium scores because smaller lesions were also selected as calcified plaques (mean variability Agatston 16.23% and volume score 18.66%). Finally, the use of interpolation had a large negative effect on the volume score (mean variability -29.67%) and almost no effect on the Agatston score. Parameter settings in software for quantification for coronary calcification affect the calcium score outcome. Therefore, parameter settings for calcium scoring should be standardized.