Amid widespread media coverage of cases of transverse agenesis of the upper limbs (TAUL) investigated in three French departments, the reporting of three new suspected cases of TAUL born in 2016 in the Bouches-du-Rhône raised the possibility of a new cluster. To investigate a potential excess of cases and a common environmental exposure, Santé publique France launched an investigation with the support of the two multidisciplinary prenatal diagnosis centers (CPDPN) in the Bouches-du-Rhône and the Reference Center for Developmental Anomalies and Malformation Syndromes of the Southeast. Two approaches were taken: a survey of the three families and a description of cases of ATMS born between 2014 and 2018 and identified in the databases of the Medical Information Systems Program for Medicine, Surgery, and Obstetrics (PMSI-MCO) and the multidisciplinary prenatal diagnosis centers (CPDPN). Two out of three families refused to participate in the interviews. Analysis of data regarding drinking water supply networks and industrial pollution in the Étang de Berre basin did not reveal any evidence of a common environmental exposure among the three cases. In addition to the cases of ATMS spontaneously reported to Remera (Rhône-Alpes Malformation Registry) and Santé publique France, analysis of the CPDPN and PMSI databases identified a total of 15 isolated cases of ATMS (6 confirmed cases, 5 possible cases, and 4 suspected cases) during the study period (2014–2018), representing an average annual prevalence of 1.2 cases per 10,000 births (95% CI 0.6–1.9), equivalent to the prevalences estimated for the 2009–2016 period by French registries, ranging from 0.8 in Auvergne to 1.8 in the French West Indies. These results do not support an excess of cases during the study period or a possible link to exposure to industrial emissions in the Étang de Berre area, as none of the mothers of the 15 isolated cases of ATMS resided in the area identified as exposed to this pollution. They also confirm that the identification of isolated cases of transverse agenesis of the upper limbs in the CPDPN and PMSI databases is likely incomplete compared to the census conducted by congenital malformation registries. The establishment of a national multisource surveillance system for congenital malformations at the national level, complementary to the current network of registries, should ultimately allow for a better understanding of their dynamics across the entire country and the detection of any spatial or temporal excesses.