Gillingham fell at the first hurdle in the Johnstone’s Paint Trophy despite a courageous display against Leyton Orient.

Orient were two goals ahead at the break as Shaun Batt scored from the penalty spot before adding a second in first half stoppage time.

It was rough justice on a Gills team who had dominated play during the first 45 minutes.

Batt completed his hat-trick in the second half before Bradley Dack (pictured) pulled one back for the Gills.

Boss Martin Allen had made four changes to his starting XI from the one which drew 1-1 with Bristol City at the weekend for their Trophy first round clash.

League 1 leaders Orient, who had won all five of their league matches to date, were on the back-foot for most of the half.

They started the game without the two strikers who had fired them to the top of the division, with David Mooney on the bench and Kevin Lisbie rested.

Chances fell regularly to Gillingham’s strike pairing Cody McDonald and Antonio German but neither were able to find a way through an Orient defence who were putting their bodies on the line to block a string of chances.

With 26 minutes gone Orient were ahead. A long throw into the box fell to the feet of former Gills loanee Romain Vincelot. McDonald’s challenge sent the midfielder to the floor and referee Michael Bull pointed to the spot.

Striker Batt sent Stuart Nelson – the former Orient keeper - the wrong way to put the visitors ahead against the run of play.

The goal failed to knock the Gills, who kept on pressing the Orient defence. But still the goals wouldn’t come.

It was déjà-vu for the Gills as for the second match running they conceded in first half stoppage time. Right-back Moses Odubajo crossed for Batt and he slid home Orient’s second of the game.

Orient had scored twice from their only two attempts of the half.

Steven Gregory, who had looked neat and tidy in the first half, made way at the break for Charlie Allen. An early booking in the first half left Gregory susceptible to being substituted and Allen injected extra pace for the Gills.

The Gills failed to create the chances at the start of the second half than they did the first and went further behind with 59 minutes gone. Batt ran onto a forward ball, shrugged off the attention of Leon Legge and shot low, across Nelson into the bottom corner.

Gillingham pulled a goal back with 21 minutes left. Hollands’ long throw was flicked on by Legge and 19-year-old Dack headed home for his first goal of the season.

The hosts gave Orient further problems after pulling a goal back but Orient saw the game out.

Gills: Nelson, Harriman, Martin, Legge, Barrett, Gregory (Allen 46mins), Hollands, Dack, Whelpdale (Weston 67mins), McDonald, German (Kedwell 74mins). Subs not used: Davies, Howard.

Orient: Jones, Omozusi, Obubajo, Baudry, Clarke, James, Bartley (Cox 90mins), Vincelot, Gorman (Cuthbert 81mins), Stockley, Batt (Mooney 66mins). Subs not used: Larkins, Lee.

Attendance: 1,730