To evaluate the methodological quality of clinical practice guidelines (CPGs) put into practice by the Peruvian Ministry of Health (MINSA), 17 CPGs from the ministry, published between 2009 and 2014, were independently evaluated by three methodologic experts using the AGREE II instrument. The score of AGREE II domains was low and very low in all CPGs: scope and purpose (medium, 44%), clarity of presentation (medium, 47%), participation of decision-makers (medium, 8%), methodological rigor (medium, 5%), applicability (medium, 5%), and editorial independence (medium, 8%). In conclusion, the methodological quality of CPGs implemented by the MINSA is low. Consequently, its use could not be recommended. The implementation of the methodology for the development of CPGs described in the recentlypublished CPG methodological preparation manual in Peru is a pressing need.