A surgical instrument may comprise a shaft having proximal and distal ends defining an axis therebetween. The shaft may be flexible and sized for insertion into the working channel of a flexible endoscope. The shaft may be configured to be used in conjunction with various suture anchor applicators. One suture anchor applicator may have a first tube with a first channel and a tissue penetrating tip. The first channel may be adapted to retain a second tube. The second tube may have a second channel and a blunt tip. The second channel may be adapted to retain at least one suture anchor and may include an exit port adapted for ejecting suture anchors. An alternative suture anchor applicator may comprise a first tube and a second tube with a tissue penetrating tip. The second channel is adapted to retain at least one suture anchor.