This article concerns the analysis of the Adverse Analytical Findings (AAFs) and the appropriate alterations made during the period 2005-2011, so that the Doping Control Laboratory of Athens (DCLA) obeys the updated World Anti-Doping Agency (WADA) List of Prohibited Substances. The % AAFs of the DCLA was compared with those of WADA-Accredited Laboratories. In 2008, the term Atypical Finding was introduced by the WADA representing a reported but inconclusive result. A characteristic example is when a testosterone-to-epitestosterone ratio is >4 followed by a negative gas chromatography/combustion/isotope ratio mass spectrometry result. In a total of about 30,000 athlete samples, 136 athletes were found with an increased testosterone/epitestosterone ratio and 43 with tetrahydrocannabinol metabolite (THCCOOH) of 427 reported AAFs. Twenty-one athletes in total were found positive with methylhexaneamine, the 11 found after a batch of 1000 samples was reprocessed. Besides, there were AAFs below their Minimum Required Performance Level (MRPL). The increasing need for higher detectability imposed new apparatus, e.g., liquid chromatography/quadrupole/time-of-flight mass spectrometry, whereas that for lowering the capital costs and reporting times led to the unification of the screening method which includes stimulants, diuretics, anabolics and other substances.