The planning and operation of multi-generation units needs to be properly addressed, to guarantee a correct assessment of their performance with respect to standard energy generation units. Performance indicators are defined to compare energy conversion units, and in presence of multiple outputs an allocation methodology is required. There is currently no single method to allocate input resources and impacts in cogeneration and multigeneration systems, as the number of aspects that are involved leads to different approaches. Each method provides specific advantages related to the target for which it has been defined, but attention must be paid on the entire range of boundary conditions that could affect the results. This paper evaluates the current methodologies for allocation factors calculation in Combined Heat and Power plants, to present an indication of the strengths and the limits of each approach. The methods are applied to multiple case studies, by considering the operation data from existing natural gas plants of different size, technology and conversion efficiency. The use of real data allows to consider actual situations in which the choice of the method could lead to different indications. The results show the significant variability of the allocation factors, the main drivers being the choice of the methodology itself, the conversion technology and the reference efficiency values that are set for separate production of heat and power. A discussion is proposed on the importance of defining proper methods and reference parameters, with particular attention to the applications for which the allocation factors need to be calculated and the potential effects on energy policies and regulations.