HPLC vials, caps and septa: how to choose

Updated 2026-11-11

Vials and closures are the consumable a chromatography lab reorders most often, and the wrong combination causes some of the most annoying problems: needle damage, cored septa, evaporation and ghost peaks. This guide walks through the choices in the order that matters, with example part numbers from the vials, caps & inserts category.

1. Match the vial format to your autosampler

The 2 mL screw-top vial (12 x 32 mm, 9 mm thread) is the default for most HPLC and LC-MS autosamplers, for example Agilent 2 mL Clear Screw-Top Vials, Certified, 100/pk (5182-0714). Some Shimadzu autosamplers use 1.5 mL vials, such as the Shimadzu Certified Vial Kit for LC/LC-MS, 1.5 mL (100/pk) (227-34001-01) or the compatible Altmann Analytik 1.5 mL Short-Thread Certified Vial Kit with UltraClean Seal, 100/kit (AAV22513667), and some use 8-425 caps (Thermo Scientific White Screw Caps with Septa for Shimadzu Autosamplers, 8-425, 100/pk (C4013-63W)). Check the rack and needle settings in your instrument manual before switching formats.

2. Clear or amber glass

Amber glass protects light-sensitive samples and standards (Agilent 2 mL Amber Screw-Top Vials with Write-On Spot, Certified, 100/pk (5182-0716)). A write-on spot makes manual labelling easier (Agilent 2 mL Clear Screw-Top Vials with Write-On Spot, Certified, 100/pk (5182-0715)).

3. Choose the cap and septum

• PTFE/silicone — the general-purpose septum: the PTFE face contacts the sample and the silicone reseals after piercing, e.g. Agilent Blue Screw Caps with PTFE/Red Silicone Septa, 100/pk (5182-0717) or separate Agilent 9 mm PTFE/Red Silicone Septa for Screw Caps, Certified, 100/pk (5182-0731).
• Pre-slit and bonded — pre-slit septa prevent a vacuum forming during repeated injections and reduce needle wear; bonded septa stay in the cap. Example: Agilent Blue Screw Caps, Bonded Pre-Slit PTFE/Silicone Septa, Certified, 100/pk (5185-5824).
• Vial/cap kits — pre-assembled kits save time and guarantee a matched fit, e.g. Thermo Scientific SureSTART 2 mL Clear Screw Vial Kit, Level 3, Bonded Slit Septa, 100/pk (6PMSCK641W) or Waters LCGC Certified 12 x 32 mm Clear Screw-Neck Vials with Pre-Slit Caps, 100/pk (186000307C).

4. Small sample volumes: inserts and total-recovery vials

When you only have a few hundred microlitres, a glass insert lets the needle draw from a small volume: Agilent 250 µL Pulled-Point Glass Vial Inserts, 100/pk (5183-2085), Agilent 250 µL Glass Inserts with Polymer Feet, 100/pk (5181-1270) or Macherey-Nagel 0.2 mL Conical Glass Insert for Wide-Opening Vials, 100/pk (702813). Total-recovery vials such as Waters LCGC Certified Total Recovery Vials, 12 x 32 mm, 100/pk (186000384C) are shaped to minimise the volume left behind.

5. LC-MS and low-adsorption vials

For LC-MS, choose vials certified for low background, such as Waters TruView Amber LCMS Certified Vials with PTFE/Silicone Septa Caps, 100/pk (186005667CV). Low-adsorption vials (Shimadzu Shim-vial H Low-Adsorption Certified Vial Kit, 1.5 mL (100/pk) (227-34500-01)) help with analytes that stick to glass, and polypropylene vials (Shimadzu Vial Kit for PFAS Analysis, Clear Plastic, 1.5 mL (100/pk) (961-10010-34)) are used for PFAS work. Pair them with LC-MS grade solvents and filtered samples (syringe filter selection guide). Check thread and septum sizes in autosampler vial sizes & compatibility.