This study is based on a unique registry of 632 patients who underwent great saphenous vein (GSV) stripping and liberal use of subfascial endoscopic perforator vein surgery (SEPS) for minimal to severe lower limb venous insufficiency. Clinical examinations and color-coded duplex scanning were performed on a randomly selected, manageable sample of 170 limbs to assess the affect of early SEPS on junctional (saphenofemoral [SFJ] and/or saphenopopliteal [SPJ]) and perforator vein (PV) insufficiencies and superficial varicosities at a median of 6.5 years. PV incompetence was present in 68 legs (40%), as the sole transfascial insufficiency in 28 limbs and combined with SFJ or SPJ incompetence in 40 limbs. Junction incompetence alone characterized an additional 38 limbs, bringing the total transfascial insufficiency prevalence to 62%. Superficial varicosities affected 46% of limbs. Overall CEAP clinical class was unimproved beyond preoperative values. PV incompetence was associated with higher CEAP and clinical venous severity scores than were junctional insufficiencies alone. We concluded that PV incompetence alone or combined with junctional insufficiency is associated with increased symptoms and disease progression. The prevalence of SFJ, SPJ, and PV incompetence (62%) and recurrent varicosities (46%) suggests that early use of SEPS does not prevent disease progression and offers no benefit over GSV stripping in the absence of deep vein insufficiency or threatened ulceration.