Recently, new custom-fit pin guides in total knee arthroplasty (TKA) have been introduced. Use of these guides may reduce operating time. Use of the guides combined with the absence of intramedullary alignment jigs may lead to reduced blood loss and improved early outcomes. Our aim was to evaluate blood loss and early clinical outcomes in patients undergoing minimally invasive TKA using custom-fit magnetic resonance imaging (MRI)-based pin guides. A prospective study in 80 patients was carried out. Patients were divided randomly into 2 equal groups. In one group, intramedullary alignment jigs were used. In the second group, custom-fit MRI-based pin guides were used. All patients received the same cemented posterior-stabilized implant through a mini-midvastus approach. The volume in the drain bottles was recorded after 48 h. Hb loss was estimated by subtracting the postoperative from the preoperative Hb level. Transfusion requirements and surgical time were recorded. Outcome measures were Knee Society Scores (KSS), knee flexion, knee swelling and pain. There was lower mean drainage of blood in the custom-fit group (391 ml vs. 603 ml; p < 0.0001). There was no difference in estimated loss of Hb (3.6 g/dl vs. 4.1 g/dl; n.s.) and in transfusion requirements (7.5 % vs. 10 %; n.s.). Surgical time was reduced in the custom-fit group (12 min less; p = 0.001). KSS measured at week 2, 6 and 12 showed no significant difference between groups. Knee flexion measured on days 7, 10 and at week 6, 12 and knee swelling and pain measured on days 1, 3, 10 and at week 6, 12 showed no significant difference between groups. Using custom-fit pin guides reduces blood drainage, but not the estimated Hb loss in minimally invasive TKA and does not affect transfusion rate. Surgical time is reduced. There is no effect on the early clinical outcomes. Therapeutic study, Level I.