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Helical magnetic flux compression generators (MFCGs) are the most promising energy sources with respect to their current amplification and compactness. They are able of producing high current pulses required in many pulsed power applications with at least one order of magnitude higher energy density than capacitive storage with similar discharge characteristics. However, the main concern with MFCGs is their intrinsic flux loss that limits severely their performance and which is not yet well understood. In general, all flux losses have a differing degree of impact, depending on the generator's volume, current and energy amplification, size of the driven load, and angular frequency of armature-helix contact point. Although several computer models have been developed in the open literature, none of them truly quantify, starting from basic physics principles, the ohmic and intrinsic flux losses in helical MFCGs. This paper describes a novel method that provides a separate calculation of intrinsic flux losses (flux that is left behind in the conductors and lost for compression) and ohmic losses, being especially easy to implement and fast to calculate. We also provide a second method that uses a simple flux quantification, making a mathematical connection between the intrinsic flux losses, quantified by the first method, and the intrinsic flux losses observed in the generators. This second method can also be used to a priori estimate the MFCG performance. Further, we will show experimental and calculated data and discuss the physical efficiency limits and scaling of generator performance at small sizes.