| Title | Year | Notes |
| "James Penney's New Identity" | 1999, edited 2006 | The 1999 version is longer. Collected in Fresh Blood 3 (edited by Mike Ripley and Maxim Jakubowski) and in Thriller (US) |
| "Guy Walks into a Bar" | 2009 | Prequel to novel Gone Tomorrow, in The New York Times |
| "Second Son" | 2011 | Electronic short story (August 2011) |
| "Knowing you're Alive" | 2011 | With M. J. Rose. Crossover with Butterfield Institute series. Collected in In Session |
| "Everyone Talks" | 2012 | In Esquire (June 2012, US edition) |
| "Deep Down" | 2012 | Electronic short story (July 2012) |
| "High Heat" | 2013 | Electronic novella (August 2013) |
| "Good and Valuable Consideration" | 2014 | With Joseph Finder. Crossover with Nick Heller series. Collected in Face Off (edited by David Baldacci, June 2014) |
| "Not a Drill" | 2014 | Electronic short story (July 2014) |
| "No Room at the Motel" | 2014 | In Stylist (December 2014) |
| "The Picture of the Lonely Diner" | 2015 | Collected in MWA Presents Manhattan Mayhem (June 2015) |
| "Small Wars" | 2015 | Electronic short story |
| "Maybe they Have a Tradition" | 2016 | In Country Life (December 2016) |
| "Too Much Time" | 2017 | Novella |
| "Faking a Murderer" | 2017 | With Kathy Reichs. Crossover with Temperance Brennan series. Collected in Matchup (June 2017) |
| "The Christmas Scorpion" | 2017 | In The Mail on Sunday (December 2017) |
| "The Fourth Man" | 2018 | Included in Australian paperback of Past Tense |
| "Cleaning the Gold" | 2019 | With Karin Slaughter. Crossover with Will Trent series (May 2019) |
| "Smile" | 2019 | Collected in Invisible Blood (July 2019) |
| "New Kid in Town" | 2022 | Collected in Hotel California (May 2022) |
| "Many Happy Returns" | 2023 | In The Spectator (December 2023) |
| "Over Easy" | 2024 | Included in Australian paperback of Safe Enough (August 2024) |