Few details of the early life of Calungsod (spelled Calonsor in Spanish records) are known. Historical records do not mention his exact birthplace or birth date and merely identified him as "Pedro Calonsor, el Visayo". Historical research identifies Ginatilan in Cebu, Hinunangan and Hinundayan in Southern Leyte, and the Molo district of Iloilo City as possible places of origin; Loboc, Bohol also makes a claim. Of these claims, the ones from Molo, Iloilo and Ginatilan, Cebu are considered the strongest.  Proponents of an Ilonggo origin argue that in the early Spanish period, the term "Visayan" exclusively referred to people from the islands of Negros or Panay, whereas people from Cebu, Bohol and Leyte were called "Pintados". Thus, had he been born in Cebu he would have been referred to as "Calonsor El Pintado" instead of "Calonsor El Visayo"; the term "Visayan" received its present scope (i.e., including inhabitants of Cebu, Bohol and Leyte) sometime the 1700s. However, American historian and scholar John N. Schumacher, S.J. disputes the Bisaya/Pintados dichotomy claim as at that time the Pintados were also referred to as Visayans regardless of location and said Pedro "was a Visayan" and may have been but doubtfully "from the island of Cebu" or "could have come any other Visayas islands."  The Cebu camp reasoned that Ginatilan contains the highest concentrations of people surnamed Calungsod and that during the beatification process, they were the original claimants to having been Calungsod's birthplace. The Calungsod family in Iloilo also claims to be the oldest branch, based on baptismal records containing the surname "Calungsod" dating to circa 1748, compared to branches in Cebu and Leyte who possess baptismal records dating only to 1828 and 1903. Regardless of his precise origin, all four locations were within the territory of the Diocese of Cebu at the time of Calungsod's martyrdom.

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