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Abstract Background To propose a new diagnostic algorithm for candidates for Fontan and identify those who can skip cardiac catheterization (CC). Methods Forty-four candidates for Fontan (median age 4.8 years, range: 2-29 years) were prospectively evaluated by trans-thoracic echocardiography (TTE), Cardiovascular magnetic resonance (CMR) and CC. Before CC, according to clinical, echo and CMR findings, patients were divided in two groups: Group I comprised 18 patients deemed suitable for Fontan without requiring CC; group II comprised 26 patients indicated for CC either in order to detect more details, or for interventional procedures. Results In Group I ("CC not required") no unexpected new information affecting surgical planning was provided by CC. Conversely, in Group II new information was provided by CC in three patients (0 vs 11.5%, p = 0.35) and in six an interventional procedure was performed. During CC, minor complications occurred in one patient from Group I and in three from Group II (6 vs 14%, p = 0.7). Radiation Dose-Area product was similar in the two groups (Median 20 Gycm2, range: 5-40 vs 26.5 Gycm2, range: 9-270 p = 0.37). All 18 Group I patients and 19 Group II patients underwent a total cavo-pulmonary anastomosis; in the remaining seven group II patients, four were excluded from Fontan; two are awaiting Fontan; one refused the intervention. Conclusion In this paper we propose a new diagnostic algorithm in a pre-Fontan setting. An accurate non-invasive evaluation comprising TTE and CMR could select patients who can skip CC.